@prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix CommandLineBinding: <https://w3id.org/cwl/cwl#CommandLineBinding/> .
@prefix Dirent: <https://w3id.org/cwl/cwl#Dirent/> .
@prefix xsd:   <http://www.w3.org/2001/XMLSchema#> .
@prefix cwl:   <https://w3id.org/cwl/cwl#> .
@prefix Workflow: <https://w3id.org/cwl/cwl#Workflow/> .
@prefix ResourceRequirement: <https://w3id.org/cwl/cwl#ResourceRequirement/> .
@prefix sld:   <https://w3id.org/cwl/salad#> .
@prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
@prefix CommandOutputBinding: <https://w3id.org/cwl/cwl#CommandOutputBinding/> .
@prefix ns1:   <http://commonwl.org/cwltool#> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct>
        rdfs:label  "Find Naming Protein Hits for struct" ;
        cwl:in      <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/max_batch_length> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/taxon_db> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/dbsize> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/blastdb> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/blast_type> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/extra_coverage> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/soft_masking> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/compart> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/top_by_score> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/align_filter> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/no_merge> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/seg> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/scatter_gather_nchunks> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/genus_list> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/affinity> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/ids> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/blast_hits_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/evalue> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/taxid> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/comp_based_stats> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/word_size> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/max_target_seqs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/blastdb_dir> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/allow_intersection> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/lds2> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/ofmt> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/asn_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/threshold> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/max_jobs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/proteins> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/nogenbank> ;
        cwl:out     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/blast_align> ;
        cwl:run     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#compart>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-compart" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-compart" ] ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#blastdb_dir>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#ids>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#comp_based_stats>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/bacterial_hit_mapping.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "bacterial_hit_mapping" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "bacterial_hit_mapping" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/bacterial_hit_mapping.cwl#hmm_hits_mft> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/bacterial_hit_mapping.cwl#sequences> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/bacterial_hit_mapping.cwl#outfile> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/bacterial_hit_mapping.cwl#proteins> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/bacterial_hit_mapping.cwl#unicoll_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/bacterial_hit_mapping.cwl#expansion_ratio> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/bacterial_hit_mapping.cwl#align_fmt> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/bacterial_hit_mapping.cwl#hmm_hits> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/bacterial_hit_mapping.cwl#no_compart> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/bacterial_hit_mapping.cwl#nogenbank> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/bacterial_hit_mapping.cwl#seq_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/bacterial_hit_mapping.cwl#asn_cache> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/bacterial_hit_mapping.cwl#aligns> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMax  4000
                                 ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ cwl:entry      "${var blob = '# aligns.mft created for bacterial_hit_mapping from input hmm_hits Array of Files\\n'; for (var i = 0; i < inputs.hmm_hits.length; i++) { blob += inputs.hmm_hits[i].path + '\\n'; } return blob; }" ;
                                                  cwl:entryname  "aligns.mft"
                                                ]
                                 ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/nogenbank>
        sld:default  true .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/word_size>
        sld:default  5 .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#blastdb_dir>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl#lds2>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-lds2" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#workers>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-workers" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-workers" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/genus_list>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#genus_list> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/split_jobs/cat_array_of_files.cwl#files_in>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl#hits_output_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-hits-output" ] ;
        sld:default       "retrieved_hits.asn" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#gpx_qsubmit/nogenbank>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#nogenbank> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#cluster_and_qdump/nogenbank>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#nogenbank> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl#hits_output>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.hits_output_name)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#lds2>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#cluster_and_qdump/word_size>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#word_size> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#retrieve_cached_hits/lds2>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#lds2> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#extra_coverage>
        sld:type  xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/set_operation.cwl#A_impl>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-A-manifest" ] ;
        sld:default       "A.mft" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/allow_intersection>
        sld:default  false .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#max_batch_length>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-max-batch-length" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-max-batch-length" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/lds2>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#lds2> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/dbsize>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#dbsize> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/blastdb_dir>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#blastdb_dir> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#cluster_and_qdump/ofmt>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#ofmt> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#output_xml_jobs>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-o" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-o" ] ;
        sld:default       "jobs.xml" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#xml_jobs>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-xml-jobs" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-xml-jobs" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#blastdb>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/separate_plasmid_orfs.cwl#plasmid_orfs>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.plasmid_orfs_out)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl#not_found_output>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.not_found_output_name)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#cluster_and_qdump/no_merge>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#no_merge> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/allow_intersection>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#allow_intersection> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#lds2>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-lds2" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-lds2" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/dbsize>
        sld:default  "6000000000" .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Map_Naming_Hits/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#sequence_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#unicoll_cache> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#retrieve_cached_hits/taxon_db>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#taxon_db> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/extra_coverage>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#extra_coverage> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Remove_off_frame_ORFs>
        rdfs:label  "Remove off-frame ORFs" ;
        cwl:in      <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Remove_off_frame_ORFs/B> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Remove_off_frame_ORFs/A> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Remove_off_frame_ORFs/operation> ;
        cwl:out     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Remove_off_frame_ORFs/output> ;
        cwl:run     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/set_operation.cwl> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/ofmt>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#ofmt> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#allow_intersection>
        sld:type  xsd:boolean .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#cluster_and_qdump/short_protein_threshold>
        sld:default  30 .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#cluster_and_qdump/dbsize>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#dbsize> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#genus_list>
        sld:type  [ sld:items  xsd:int ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/blastdb>
        sld:default  "blast_rules_db" , "blastdb" .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#affinity>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-affinity" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-affinity" ] ;
        sld:default       "subject" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/separate_plasmid_orfs.cwl#plasmid_orfs_out>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-plasmid_orfs" ] ;
        sld:default       "plasmid_orf.ids" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/blastdb_dir>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#blastdb_dir> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#delay>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-delay" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-delay" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/split_jobs/split.cwl#suffix>
        cwl:inputBinding  [ CommandLineBinding:position  3 ;
                            CommandLineBinding:prefix    "--additional-suffix=" ;
                            CommandLineBinding:separate  false
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  3 ;
                            CommandLineBinding:prefix    "--additional-suffix=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:default       ".xml" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#asn_cache>
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    "," ;
                            CommandLineBinding:prefix  "-asn-cache"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    "," ;
                            CommandLineBinding:prefix  "-asn-cache"
                          ] ;
        sld:type          [ sld:items  cwl:Directory ;
                            sld:type   sld:array
                          ] ;
        sld:type          [ sld:items  cwl:Directory ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/top_by_score>
        sld:default  10 .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#retrieve_cached_hits>
        cwl:in   <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#retrieve_cached_hits/proteins> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#retrieve_cached_hits/lds2> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#retrieve_cached_hits/taxid> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#retrieve_cached_hits/genus_list> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#retrieve_cached_hits/blast_type> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#retrieve_cached_hits/taxon_db> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#retrieve_cached_hits/sqlite_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#retrieve_cached_hits/orfs> ;
        cwl:out  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#retrieve_cached_hits/not_found_output> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#retrieve_cached_hits/hits_output> ;
        cwl:run  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#gpx_qsubmit/batch_size>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#batch-size> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#short_protein_threshold>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-short-protein-threshold" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-short-protein-threshold" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/split_jobs/split.cwl#chunk_size>
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "-l"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "-l"
                          ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/compart>
        sld:default  false .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/max_jobs>
        sld:default  1 .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#prot_ids_A>
        rdfs:label  "Extract ORF Proteins/prot_ids" ;
        sld:type    cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#lds2>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-lds2" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-lds2" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#genus_list>
        sld:type  [ sld:items  xsd:int ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#cluster_and_qdump/max_jobs>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#max_jobs> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#gpx_qsubmit>
        cwl:in   <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#gpx_qsubmit/batch_size> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#gpx_qsubmit/nogenbank> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#gpx_qsubmit/lds2> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#gpx_qsubmit/max_batch_length> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#gpx_qsubmit/asn_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#gpx_qsubmit/ids> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#gpx_qsubmit/affinity> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#gpx_qsubmit/blastdb_dir> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#gpx_qsubmit/proteins> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#gpx_qsubmit/blastdb> ;
        cwl:out  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#gpx_qsubmit/jobs> ;
        cwl:run  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#subseq_size>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-subseq-size" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-subseq-size" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#nogenbank>
        sld:type  xsd:boolean .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#jobs>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output_xml_jobs)" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output_xml_jobs)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#cluster_and_qdump/evalue>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#evalue> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#collect_aligns/files_in>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#cluster_and_qdump/blast_align> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/blast_type>
        sld:default  "orf" .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Remove_off_frame_ORFs/B>
        cwl:linkMerge  "merge_flattened" ;
        cwl:source     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#prot_ids_B1> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#prot_ids_B2> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#word_size>
        sld:type  xsd:int .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#dbsize>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Separate_Plasmid_ORFs/orf_ids>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Remove_off_frame_ORFs/output> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#gpx_qdump>
        cwl:in   <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#gpx_qdump/input_path> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#gpx_qdump/unzip> ;
        cwl:out  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#gpx_qdump/output> ;
        cwl:run  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qdump.cwl> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#threshold>
        sld:type  xsd:int .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#dbsize>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-dbsize" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-dbsize" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Separate_Plasmid_ORFs/plasmids>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#plasmids> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#gpx_qsubmit/proteins>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#proteins> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#taxid>
        sld:type  xsd:int .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/top_by_score>
        sld:default  10 .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/comp_based_stats>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#comp_based_stats> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#ofmt>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#evalue>
        sld:type  xsd:float , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/lds2>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#lds2> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/threshold>
        sld:default  20 .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/no_merge>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#no_merge> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/blast_hits_cache>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#blast_hits_cache> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/taxon_db>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#taxon_db> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#compart>
        sld:type  xsd:boolean .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#gpx_qsubmit/proteins>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#proteins> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#seg>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#allow_intersection>
        sld:type  xsd:boolean .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/top_by_score>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#top_by_score> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/taxid>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#taxid> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#asn_cache> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Map_Naming_Hits/proteins>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#proteins> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#cluster_and_qdump/proteins>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#proteins> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/separate_plasmid_orfs.cwl#plasmids>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-plasmids" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#overlap>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-overlap" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-overlap" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#batch_size>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-batch-size" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-batch-size" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Remove_off_frame_ORFs/operation>
        sld:default  "-" .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#cluster_and_qdump/input_jobs>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#split_jobs/jobs> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#align_filter>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/compart>
        sld:default  false .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#collect_aligns/files_in>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/blast_align> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Map_Naming_Hits/expansion_ratio>
        sld:default  1.1e+00 .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#blastdb>
        rdfs:label  "Input blastdb databases" ;
        sld:type    [ sld:items  xsd:string ;
                      sld:type   sld:array
                    ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/align_filter>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#align_filter> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#no_merge>
        sld:type  xsd:boolean .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#blast_hits_cache>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/max_jobs>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#max_jobs> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#plasmids>
        rdfs:label  "Prepare_Unannotated_Sequences/plasmids" ;
        sld:type    cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl#taxid>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-taxid" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#queries_gc_id_list>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-queries-gc-id-list" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-queries-gc-id-list" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Map_Naming_Hits/sequences>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#annotation> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#max_target_seqs>
        sld:type  xsd:int .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#asn_cache>
        sld:type  [ sld:items  cwl:Directory ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#extra_coverage>
        sld:type  xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#cluster_and_qdump/blastdb_dir>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#blastdb_dir> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#genus_list>
        sld:type  [ sld:items  xsd:int ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#no_merge>
        sld:type  xsd:boolean .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#split_jobs/input>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#gpx_qsubmit/jobs> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/seg>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#seg> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Separate_Plasmid_ORFs>
        rdfs:label  "Separate Plasmid ORFs" ;
        cwl:in      <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Separate_Plasmid_ORFs/orf_entries> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Separate_Plasmid_ORFs/raw_seqs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Separate_Plasmid_ORFs/orf_ids> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Separate_Plasmid_ORFs/plasmids> ;
        cwl:out     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Separate_Plasmid_ORFs/chomosome_orfs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Separate_Plasmid_ORFs/plasmid_orfs> ;
        cwl:run     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/separate_plasmid_orfs.cwl> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/lds2>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#lds2> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/dbsize>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#dbsize> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/max_target_seqs>
        sld:default  50 .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/set_operation.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "set_operation" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "set_operation" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/set_operation.cwl#B_impl> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/set_operation.cwl#B> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/set_operation.cwl#output_impl> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/set_operation.cwl#operation> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/set_operation.cwl#A> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/set_operation.cwl#A_impl> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/set_operation.cwl#output> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ cwl:entry      "${var blob = '# A.mft created for set_operation from input A Array of Files\\n'; for (var i = 0; i < inputs.A.length; i++) { blob += inputs.A[i].path + '\\n'; } return blob; }" ;
                                                  cwl:entryname  "A.mft"
                                                ] ;
                                   cwl:listing  [ cwl:entry      "${var blob = '# B.mft created for set_operation from input B Array of Files\\n'; for (var i = 0; i < inputs.B.length; i++) { blob += inputs.B[i].path + '\\n'; } return blob; }" ;
                                                  cwl:entryname  "B.mft"
                                                ]
                                 ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/max_jobs>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#max_jobs> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode>
        cwl:in   <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/max_jobs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/ofmt> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/no_merge> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/blastdb_dir> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/allow_intersection> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/input_jobs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/seg> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/soft_masking> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/top_by_score> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/workers_per_cpu> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/comp_based_stats> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/max_target_seqs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/word_size> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/nogenbank> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/align_filter> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/dbsize> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/threshold> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/evalue> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/compart> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/short_protein_threshold> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/asn_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/lds2> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/extra_coverage> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/proteins> ;
        cwl:out  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/outdir> ;
        cwl:run  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/separate_plasmid_orfs.cwl#chomosome_orfs_out>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-chromosome_orfs" ] ;
        sld:default       "chromosome_orf.ids" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#annotation>
        rdfs:label  "Get ORFs/outseq" ;
        sld:type    cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl#orfs_manifest>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-orfs-manifest" ] ;
        sld:default       "ids.mft" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#gpx_qsubmit/ids>
        cwl:linkMerge  "merge_flattened" ;
        cwl:source     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#retrieve_cached_hits/not_found_output> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#max_jobs>
        sld:type  xsd:int .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/seg>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#seg> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#comp_based_stats>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/split_jobs/split.cwl#jobs>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.mask)?*$(inputs.suffix)" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.mask)?*$(inputs.suffix)" ] ;
        sld:type           [ sld:items  cwl:File ;
                             sld:type   sld:array
                           ] ;
        sld:type           [ sld:items  cwl:File ;
                             sld:type   sld:array
                           ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#asn_cache>
        sld:type  [ sld:items  cwl:Directory ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#prot_ids_B1>
        rdfs:label  "Get off-frame ORFs/prot_ids" ;
        sld:type    cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/bacterial_hit_mapping.cwl#unicoll_cache>
        sld:type  cwl:Directory , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/bacterial_hit_mapping.cwl#align_fmt>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-align-fmt" ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#blast_hits_cache>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/short_protein_threshold>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#short_protein_threshold> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/set_operation.cwl#B>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/scatter_gather_nchunks>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#scatter_gather_nchunks> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/ofmt>
        sld:default  "asn-binary" .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#align_filter>
        sld:type  xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#gpx_qsubmit/nogenbank>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#nogenbank> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/separate_plasmid_orfs.cwl#orf_ids>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-orf_ids" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#blast_align>
        cwl:outputSource  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#collect_aligns/file_out> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#retrieve_cached_hits/hits_output> ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#threshold>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-threshold" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-threshold" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl#orfs>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#gpx_qsubmit/batch_size>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#batch-size> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#dbsize>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/blastdb_dir>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#identification_db_dir> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/bacterial_hit_mapping.cwl#outfile>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-o" ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#max_jobs>
        sld:type  xsd:int .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qdump.cwl#output_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-output" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-output" ] ;
        sld:default       "output.asn" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/bacterial_hit_mapping.cwl#seq_cache>
        sld:type  cwl:Directory , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#scatter_gather_nchunks>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#asn_cache>
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    "," ;
                            CommandLineBinding:prefix  "-asn-cache"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    "," ;
                            CommandLineBinding:prefix  "-asn-cache"
                          ] ;
        sld:type          sld:null ;
        sld:type          [ sld:items  cwl:Directory ;
                            sld:type   sld:array
                          ] ;
        sld:type          [ sld:items  cwl:Directory ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/proteins>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#proteins> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/seg>
        sld:default  "30 2.2 2.5" .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#NxM_threshold>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-NxM-threshold" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-NxM-threshold" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#cluster_and_qdump/max_target_seqs>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#max_target_seqs> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/separate_plasmid_orfs.cwl#orf_entries>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-orf_entries" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl#proteins>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "blastp_wnode_struct" ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#collect_aligns> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#split_jobs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#cluster_and_qdump> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#gpx_qsubmit> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#nogenbank> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#blast_type> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#allow_intersection> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#max_batch_length> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#blast_hits_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#word_size> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#lds2> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#batch-size> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#max_target_seqs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#max_jobs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#top_by_score> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#evalue> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#ofmt> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#seg> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#no_merge> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#threshold> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#ids> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#extra_coverage> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#soft_masking> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#blastdb_dir> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#dbsize> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#proteins> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#taxid> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#affinity> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#asn_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#scatter_gather_nchunks> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#genus_list> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#align_filter> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#taxon_db> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#compart> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#comp_based_stats> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#blastdb> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#blast_align> ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:ScatterFeatureRequirement ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#asn_cache> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#retrieve_cached_hits/orfs>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#ids> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#workers_per_cpu>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-workers-per-cpu" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-workers-per-cpu" ] ;
        sld:type          xsd:float , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/max_target_seqs>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#max_target_seqs> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#cluster_and_qdump/comp_based_stats>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#comp_based_stats> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/split_jobs/split.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "cwl split wrapper" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "split" ) ;
        cwl:baseCommand          ( "split" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/split_jobs/split.cwl#mask> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/split_jobs/split.cwl#suffix> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/split_jobs/split.cwl#input> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/split_jobs/split.cwl#nchunks> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/split_jobs/split.cwl#chunk_size> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/split_jobs/split.cwl#jobs> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#extra_coverage>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-extra-coverage" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-extra-coverage" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#gpx_qsubmit/affinity>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#affinity> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl#not_found_output_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-not-found-output" ] ;
        sld:default       "not_found.ids" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#cluster_and_qdump/seg>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#seg> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl#genus_list>
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    "," ;
                            CommandLineBinding:prefix  "-genus-list"
                          ] ;
        sld:type          sld:null ;
        sld:type          [ sld:items  xsd:int ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#lds2>
        rdfs:label  "Extract ORF Proteins/lds2" ;
        sld:type    cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#evalue>
        sld:type  xsd:float , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#nogenbank>
        sld:type  xsd:boolean .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#gpx_qsubmit/blastdb>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#blastdb> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/bacterial_hit_mapping.cwl#proteins>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/bacterial_hit_mapping.cwl#aligns>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.outfile)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#proteins>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#allow_intersection>
        sld:type  xsd:boolean .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#soft_masking>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/input_jobs>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#input_jobs> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "cluster_blastp_wnode and gpx_qdump combined" ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#gpx_qdump> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#nogenbank> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#ofmt> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#blastdb_dir> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#max_jobs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#short_protein_threshold> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#word_size> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#seg> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#extra_coverage> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#max_target_seqs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#no_merge> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#asn_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#proteins> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#comp_based_stats> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#input_jobs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#soft_masking> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#evalue> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#compart> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#align_filter> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#top_by_score> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#allow_intersection> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#threshold> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#lds2> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#dbsize> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#blast_align> ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/soft_masking>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#soft_masking> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#ids>
        sld:type  sld:null ;
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/max_batch_length>
        sld:default  10000 .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#gpx_qsubmit/affinity>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#affinity> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#sequence_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#unicoll_cache> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#blast_hits_cache>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#top_by_score>
        sld:type  xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#cluster_and_qdump/lds2>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#lds2> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#ofmt>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/seg>
        sld:default  "30 2.2 2.5" .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "Bacterial Annotation, pass 2, blastp-based functional annotation (first pass)" ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Remove_off_frame_ORFs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Map_Naming_Hits> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Separate_Plasmid_ORFs> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#taxon_db> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#prot_ids_B2> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#identification_db_dir> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#blast_rules_db> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#prot_ids_B1> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#blastdb> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#raw_seqs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#genus_list> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#scatter_gather_nchunks> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#taxid> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#plasmids> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#blast_hits_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#proteins> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#prot_ids_A> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#annotation> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#sequence_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#unicoll_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#lds2> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#aligns> ;
        cwl:requirements         [ a  cwl:MultipleInputFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#nogenbank>
        sld:type  xsd:boolean .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/split_jobs/split.cwl#input>
        cwl:inputBinding  [ CommandLineBinding:position
                          4 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          4 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#proteins>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/blastdb_dir>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#identification_db_dir> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/workers_per_cpu>
        sld:default  1e+00 .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/split_jobs/split.cwl#nchunks>
        cwl:inputBinding  [ CommandLineBinding:position  2 ;
                            CommandLineBinding:prefix    "-n l//" ;
                            CommandLineBinding:separate  false
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  2 ;
                            CommandLineBinding:prefix    "-n l//" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qdump.cwl#input_path>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input-path" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input-path" ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/threshold>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#threshold> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/no_merge>
        sld:default  true .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#taxid>
        sld:type  xsd:int .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#collect_aligns>
        cwl:in   <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#collect_aligns/files_in> ;
        cwl:out  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#collect_aligns/file_out> ;
        cwl:run  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/split_jobs/cat_array_of_files.cwl> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/extra_coverage>
        sld:default  20 .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#align_filter>
        sld:type  xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#blastdb_dir>
        sld:type  cwl:Directory , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Map_Naming_Hits/outfile>
        sld:default  "mapped-aligns.asn" .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#cluster_and_qdump/align_filter>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#align_filter> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#sequence_cache>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qdump.cwl#output>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output_name)" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output_name)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/taxid>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#taxid> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/bacterial_hit_mapping.cwl#asn_cache>
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    "," ;
                            CommandLineBinding:prefix  "-asn-cache"
                          ] ;
        sld:type          [ sld:items  cwl:Directory ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#nogenbank>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-nogenbank" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-nogenbank" ] ;
        sld:default       true ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#no_merge>
        sld:type  xsd:boolean .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/set_operation.cwl#B_impl>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-B-manifest" ] ;
        sld:default       "B.mft" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/nogenbank>
        sld:default  true .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#batch-size>
        sld:type  xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#gpx_qsubmit/lds2>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#lds2> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qdump.cwl#unzip>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-unzip" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-unzip" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#blastdb>
        cwl:inputBinding  [ CommandLineBinding:prefix  "-db" ;
                            cwl:valueFrom              "${ var blob = ''; for (var i = 0; i < inputs.blastdb.length; i++) { blob += inputs.blastdb_dir.path + '/' + inputs.blastdb[i]; if(i != inputs.blastdb.length-1) blob += ','; } return blob; }"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix  "-db" ;
                            cwl:valueFrom              "${ var blob = ''; for (var i = 0; i < inputs.blastdb.length; i++) { blob += inputs.blastdb_dir.path + '/' + inputs.blastdb[i]; if(i != inputs.blastdb.length-1) blob += ','; } return blob; }"
                          ] ;
        sld:type          sld:null ;
        sld:type          [ sld:items  xsd:string ;
                            sld:type   sld:array
                          ] ;
        sld:type          [ sld:items  xsd:string ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/word_size>
        sld:default  5 .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:comment             "This workflow is specialized for the case when there is an LDS2 input  LDS2 is a _reference_ object, the kind that CWL does not like we need to provide actual input: proteins which matches the name of ASN.1 object references in LDS2 Another limitation is that it can handle no more than two item arrays in blastdb_dir and asn_cache Workaround used so far: in:\n  proteins:\n    default:\n        class: File\n        path: '/dev/null'\n        basename: 'null'\n        contents: ''\n" ;
        rdfs:label               "gpx_qsubmit" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "gpx_qsubmit" ) ;
        cwl:baseCommand          ( "gpx_qsubmit" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#asn_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#ids_manifest> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#max_batch_length> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#queries_gc_id_list> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#output_xml_jobs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#xml_jobs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#NxM_threshold> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#proteins> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#subseq_size> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#lds2> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#affinity> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#batch_size> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#blastdb_dir> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#ids> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#nogenbank> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#overlap> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#subjects_gc_id_list> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#blastdb> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#jobs> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ cwl:entry      "${var blob = '# ids.mft created for gpx_qsubmit from input ids Array of Files\\n';for (var i = 0; i < inputs.ids.length; i++) {blob += inputs.ids[i].path  + '\\n';}return blob;}" ;
                                                  cwl:entryname  "ids.mft"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "${ var cs=0; var s=inputs.asn_cache.length-1; var as = cs; if(as >= s) {as = s }; return inputs.asn_cache[as]; }"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.proteins)"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.blastdb_dir)"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "${ var cs=1; var s=inputs.asn_cache.length-1; var as = cs; if(as >= s) {as = s }; return inputs.asn_cache[as]; }"
                                                ]
                                 ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.proteins)"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.blastdb_dir)"
                                                ] ;
                                   cwl:listing  [ cwl:entry      "${var blob = '# ids.mft created for gpx_qsubmit from input ids Array of Files\\n';for (var i = 0; i < inputs.ids.length; i++) {blob += inputs.ids[i].path  + '\\n';}return blob;}" ;
                                                  cwl:entryname  "ids.mft"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "${ var cs=0; var s=inputs.asn_cache.length-1; var as = cs; if(as >= s) {as = s }; return inputs.asn_cache[as]; }"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "${ var cs=1; var s=inputs.asn_cache.length-1; var as = cs; if(as >= s) {as = s }; return inputs.asn_cache[as]; }"
                                                ]
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#soft_masking>
        sld:type  xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#threshold>
        sld:type  xsd:int .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#seg>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/split_jobs/cat_array_of_files.cwl#file_out>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "cat.out" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "cat.out" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#split_jobs/input>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#gpx_qsubmit/jobs> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#identification_db_dir>
        rdfs:label  "Create identification BLASTdb" ;
        sld:type    cwl:Directory .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/compart>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#compart> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/dbsize>
        sld:default  "6000000000" .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Remove_off_frame_ORFs/A>
        cwl:linkMerge  "merge_flattened" ;
        cwl:source     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#prot_ids_A> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#max_jobs>
        sld:type  xsd:int .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/align_filter>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#align_filter> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#dbsize>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#no_merge>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-no-merge" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-no-merge" ] ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#gpx_qdump/unzip>
        sld:default  "*" .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/no_merge>
        sld:default  true .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#lds2>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "cluster_blastp_wnode" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "cluster_blastp_wnode" ) ;
        cwl:baseCommand          ( "cluster_blastp_wnode" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#short_protein_threshold> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#allow_intersection> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#backlog> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#asn_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#ofmt> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#soft_masking> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#workers> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#nogenbank> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#lds2> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#seg> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#output_dir> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#workers_per_cpu> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#top_by_score> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#extra_coverage> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#evalue> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#comp_based_stats> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#input_jobs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#max_target_seqs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#max_jobs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#dbsize> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#no_merge> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#word_size> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#blastdb_dir> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#align_filter> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#compart> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#delay> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#threshold> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#proteins> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#outdir> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "${ var cs=0; var s=inputs.asn_cache.length-1; var as = cs; if(as >= s) {as = s }; return inputs.asn_cache[as]; }"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.proteins)"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.blastdb_dir)"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "${ var cs=1; var s=inputs.asn_cache.length-1; var as = cs; if(as >= s) {as = s }; return inputs.asn_cache[as]; }"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  true ;
                                                  cwl:entry        "$(inputs.lds2)"
                                                ]
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMax  5000
                                 ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "${ var cs=0; var s=inputs.asn_cache.length-1; var as = cs; if(as >= s) {as = s }; return inputs.asn_cache[as]; }"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  true ;
                                                  cwl:entry        "$(inputs.lds2)"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.proteins)"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "${ var cs=1; var s=inputs.asn_cache.length-1; var as = cs; if(as >= s) {as = s }; return inputs.asn_cache[as]; }"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.blastdb_dir)"
                                                ]
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMax  5000
                                 ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/set_operation.cwl#operation>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-operation" ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#gpx_qsubmit/blastdb_dir>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#blastdb_dir> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#compart>
        sld:type  xsd:boolean .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#retrieve_cached_hits/taxid>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#taxid> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#blast_align>
        cwl:outputSource  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#cluster_and_qdump/blast_align> ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#gpx_qsubmit/max_batch_length>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#max_batch_length> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/max_target_seqs>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#max_target_seqs> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#asn_cache>
        sld:type  [ sld:items  cwl:Directory ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  cwl:Directory ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#retrieve_cached_hits/proteins>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#proteins> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#input_jobs>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/comp_based_stats>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#comp_based_stats> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#scatter_gather_nchunks>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#collect_aligns>
        cwl:in   <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#collect_aligns/files_in> ;
        cwl:out  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#collect_aligns/file_out> ;
        cwl:run  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/split_jobs/cat_array_of_files.cwl> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#backlog>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-backlog" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-backlog" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#retrieve_cached_hits/blast_type>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#blast_type> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/evalue>
        sld:default  1e-01 .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Map_Naming_Hits/no_compart>
        sld:default  false .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/split_jobs/split.cwl#mask>
        cwl:inputBinding  [ CommandLineBinding:position  5 ;
                            cwl:valueFrom                "$(inputs.mask)"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  5 ;
                            cwl:valueFrom                "$(inputs.mask)"
                          ] ;
        sld:default       "jobs" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/bacterial_hit_mapping.cwl#nogenbank>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-nogenbank" ] ;
        sld:type          xsd:boolean .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Map_Naming_Hits/nogenbank>
        sld:default  true .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#top_by_score>
        sld:type  xsd:int .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/input_jobs>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#split_jobs/jobs> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#max_jobs>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-max-jobs" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-max-jobs" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/threshold>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#threshold> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/max_jobs>
        sld:default  1 .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qdump.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "gpx_qdump" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-produce-empty-file" ) ;
        cwl:arguments            ( "-produce-empty-file" ) ;
        cwl:baseCommand          ( "gpx_qdump" ) ;
        cwl:baseCommand          ( "gpx_qdump" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qdump.cwl#input_path> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qdump.cwl#unzip> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qdump.cwl#output_name> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qdump.cwl#output> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#gpx_qsubmit/ids>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#ids> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/proteins>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#proteins> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/bacterial_hit_mapping.cwl#hmm_hits>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#proteins>
        rdfs:label  "Extract ORF Proteins/proteins" ;
        sld:type    cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#max_target_seqs>
        sld:type  xsd:int .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#seg>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#ofmt>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#nogenbank>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-nogenbank" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-nogenbank" ] ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#affinity>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl#blast_type>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-blast-type" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#output_dir>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-O" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-O" ] ;
        sld:default       "output" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#word_size>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-word_size" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-word_size" ] ;
        sld:type          xsd:int .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#cluster_and_qdump/extra_coverage>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#extra_coverage> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#proteins>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#soft_masking>
        sld:type  xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#cluster_and_qdump/soft_masking>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#soft_masking> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/allow_intersection>
        sld:default  false .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#ids>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#unicoll_cache>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/no_merge>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#no_merge> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#max_batch_length>
        sld:type  xsd:int .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#seg>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-seg" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-seg" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#top_by_score>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-top-by-score" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-top-by-score" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#gpx_qsubmit/blastdb_dir>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#blastdb_dir> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#affinity>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/evalue>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#evalue> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids>
        rdfs:label  "Find Struct Protein Hits for Plasmids" ;
        cwl:in      <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/affinity> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/blast_type> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/seg> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/asn_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/blastdb> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/max_jobs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/blast_hits_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/nogenbank> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/dbsize> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/top_by_score> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/taxon_db> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/ofmt> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/extra_coverage> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/soft_masking> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/threshold> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/align_filter> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/max_batch_length> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/allow_intersection> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/proteins> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/compart> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/taxid> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/ids> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/lds2> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/word_size> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/comp_based_stats> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/evalue> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/max_target_seqs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/scatter_gather_nchunks> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/genus_list> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/blastdb_dir> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/no_merge> ;
        cwl:out     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/blast_align> ;
        cwl:run     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/taxon_db>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#taxon_db> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/set_operation.cwl#output>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output_impl)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/threshold>
        sld:default  20 .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/bacterial_hit_mapping.cwl#sequences>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-sequences" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/max_target_seqs>
        sld:default  50 .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#taxon_db>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#comp_based_stats>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-comp_based_stats" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-comp_based_stats" ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/evalue>
        sld:default  1e-01 .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "orf_hits_cache_retrieve" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-nogenbank" ) ;
        cwl:baseCommand          ( "orf_hits_cache_retrieve" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl#proteins> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl#genus_list> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl#lds2> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl#orfs_manifest> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl#taxon_db> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl#blast_type> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl#not_found_output_name> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl#sqlite_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl#taxid> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl#orfs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl#hits_output_name> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl#not_found_output> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl#hits_output> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.proteins)"
                                                ] ;
                                   cwl:listing  [ cwl:entry      "${\n  var blob = '# ids.mft created for orf_hits_cache_retrieve from input \"orfs\" Array of Files' +\n    String.fromCharCode(10) ; \n  for (var i = 0; i < inputs.orfs.length; i++) { \n    blob += inputs.orfs[i].path + String.fromCharCode(10); \n  } \n  return blob; \n}" ;
                                                  cwl:entryname  "ids.mft"
                                                ]
                                 ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#blastdb_dir>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#align_filter>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-align_filter" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-align_filter" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/align_filter>
        sld:default  "score>0 && pct_identity_gapopen_only > 35" .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#blast_align>
        cwl:outputSource  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#gpx_qdump/output> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Separate_Plasmid_ORFs/orf_entries>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#annotation> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/separate_plasmid_orfs.cwl#chomosome_orfs>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.chomosome_orfs_out)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#proteins>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#max_target_seqs>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-max_target_seqs" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-max_target_seqs" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#cluster_and_qdump/threshold>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#threshold> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/proteins>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#proteins> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#top_by_score>
        sld:type  xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#ofmt>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-ofmt" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-ofmt" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#split_jobs/nchunks>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#scatter_gather_nchunks> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/compart>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#compart> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/soft_masking>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#soft_masking> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/lds2>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#lds2> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#gpx_qsubmit/lds2>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#lds2> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/set_operation.cwl#A>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#taxid>
        sld:type  xsd:int .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/comp_based_stats>
        sld:default  "F" .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/comp_based_stats>
        sld:default  "F" .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#scatter_gather_nchunks>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#cluster_and_qdump/allow_intersection>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#allow_intersection> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#ids_manifest>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-ids-manifest" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-ids-manifest" ] ;
        sld:default       "ids.mft" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/nogenbank>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#nogenbank> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#blastdb_dir>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#aligns>
        rdfs:label        "goes to protein_alignment/Seed Search Compartments/compartments" ;
        cwl:outputSource  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Map_Naming_Hits/aligns> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/word_size>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#word_size> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/ofmt>
        sld:default  "asn-binary" .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/align_filter>
        sld:default  "score>0 && pct_identity_gapopen_only > 35" .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#evalue>
        sld:type  xsd:float , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#retrieve_cached_hits/genus_list>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#genus_list> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#evalue>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-evalue" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-evalue" ] ;
        sld:type          xsd:float , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/set_operation.cwl#output_impl>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-output" ] ;
        sld:default       "result.lst" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/blast_hits_cache>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#blast_hits_cache> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/allow_intersection>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#allow_intersection> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#subjects_gc_id_list>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-subjects-gc-id-list" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-subjects-gc-id-list" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump>
        cwl:in       <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/extra_coverage> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/top_by_score> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/proteins> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/lds2> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/max_target_seqs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/ofmt> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/word_size> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/evalue> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/input_jobs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/max_jobs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/dbsize> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/allow_intersection> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/asn_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/align_filter> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/nogenbank> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/compart> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/seg> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/comp_based_stats> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/soft_masking> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/no_merge> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/blastdb_dir> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/threshold> ;
        cwl:out      <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/blast_align> ;
        cwl:run      <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl> ;
        cwl:scatter  ( <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/input_jobs> ) .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#gpx_qsubmit/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#asn_cache> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#cluster_and_qdump>
        cwl:in       <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#cluster_and_qdump/extra_coverage> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#cluster_and_qdump/nogenbank> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#cluster_and_qdump/threshold> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#cluster_and_qdump/soft_masking> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#cluster_and_qdump/top_by_score> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#cluster_and_qdump/align_filter> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#cluster_and_qdump/comp_based_stats> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#cluster_and_qdump/allow_intersection> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#cluster_and_qdump/lds2> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#cluster_and_qdump/asn_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#cluster_and_qdump/seg> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#cluster_and_qdump/word_size> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#cluster_and_qdump/blastdb_dir> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#cluster_and_qdump/proteins> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#cluster_and_qdump/evalue> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#cluster_and_qdump/compart> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#cluster_and_qdump/max_target_seqs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#cluster_and_qdump/short_protein_threshold> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#cluster_and_qdump/input_jobs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#cluster_and_qdump/max_jobs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#cluster_and_qdump/ofmt> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#cluster_and_qdump/dbsize> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#cluster_and_qdump/no_merge> ;
        cwl:out      <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#cluster_and_qdump/blast_align> ;
        cwl:run      <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl> ;
        cwl:scatter  ( <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#cluster_and_qdump/input_jobs> ) .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#comp_based_stats>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#gpx_qdump/input_path>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/outdir> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/ofmt>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#ofmt> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/ids>
        cwl:linkMerge  "merge_flattened" ;
        cwl:source     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Separate_Plasmid_ORFs/plasmid_orfs> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Separate_Plasmid_ORFs/raw_seqs>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#raw_seqs> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Map_Naming_Hits>
        rdfs:label  "Map Naming Hits" ;
        cwl:in      <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Map_Naming_Hits/sequences> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Map_Naming_Hits/align_fmt> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Map_Naming_Hits/proteins> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Map_Naming_Hits/outfile> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Map_Naming_Hits/expansion_ratio> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Map_Naming_Hits/asn_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Map_Naming_Hits/hmm_hits> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Map_Naming_Hits/no_compart> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Map_Naming_Hits/nogenbank> ;
        cwl:out     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Map_Naming_Hits/aligns> ;
        cwl:run     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/bacterial_hit_mapping.cwl> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#outdir>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output_dir)" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output_dir)" ] ;
        sld:type           cwl:Directory .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/proteins>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#proteins> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "blastp_wnode_naming" ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#gpx_qsubmit> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#collect_aligns> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#retrieve_cached_hits> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#split_jobs> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#max_target_seqs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#blastdb_dir> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#evalue> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#ofmt> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#allow_intersection> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#align_filter> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#taxid> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#soft_masking> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#dbsize> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#top_by_score> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#asn_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#compart> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#max_batch_length> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#word_size> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#lds2> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#blastdb> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#ids> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#comp_based_stats> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#taxon_db> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#nogenbank> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#affinity> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#genus_list> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#proteins> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#threshold> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#extra_coverage> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#scatter_gather_nchunks> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#blast_hits_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#max_jobs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#blast_type> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#seg> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#no_merge> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#batch-size> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#blast_align> ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:ScatterFeatureRequirement ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/separate_plasmid_orfs.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "separate_plasmid_orfs" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "separate_plasmid_orfs" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/separate_plasmid_orfs.cwl#plasmids> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/separate_plasmid_orfs.cwl#raw_seqs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/separate_plasmid_orfs.cwl#orf_ids> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/separate_plasmid_orfs.cwl#orf_entries> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/separate_plasmid_orfs.cwl#plasmid_orfs_out> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/separate_plasmid_orfs.cwl#chomosome_orfs_out> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/separate_plasmid_orfs.cwl#chomosome_orfs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/separate_plasmid_orfs.cwl#plasmid_orfs> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#lds2>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#compart>
        sld:type  xsd:boolean .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#word_size>
        sld:type  xsd:int .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#gpx_qsubmit/blastdb>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#blastdb> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#threshold>
        sld:type  xsd:int .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/blast_type>
        sld:default  "orf" .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#blastdb>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#cluster_and_qdump/compart>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#compart> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl#taxon_db>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-taxon-db" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/max_batch_length>
        sld:default  10000 .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl#proteins>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/bacterial_hit_mapping.cwl#hmm_hits_mft>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-aligns-manifest" ] ;
        sld:default       "aligns.mft" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#allow_intersection>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-allow-intersection" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-allow-intersection" ] ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/affinity>
        sld:default  "subject" .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#cluster_and_qdump/top_by_score>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#top_by_score> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#short_protein_threshold>
        sld:type  xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Map_Naming_Hits/hmm_hits>
        cwl:linkMerge  "merge_flattened" ;
        cwl:source     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/blast_align> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/blast_align> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#split_jobs/nchunks>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#scatter_gather_nchunks> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#word_size>
        sld:type  xsd:int .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/separate_plasmid_orfs.cwl#raw_seqs>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-raw_seqs" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#blast_rules_db>
        rdfs:label   "parameter to store the literal 'blast_rules_db'" ;
        sld:default  "blast_rules_db" ;
        sld:type     xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/genus_list>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#genus_list> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#gpx_qsubmit/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#asn_cache> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#gpx_qsubmit>
        cwl:in   <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#gpx_qsubmit/batch_size> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#gpx_qsubmit/blastdb> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#gpx_qsubmit/lds2> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#gpx_qsubmit/proteins> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#gpx_qsubmit/max_batch_length> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#gpx_qsubmit/asn_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#gpx_qsubmit/affinity> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#gpx_qsubmit/nogenbank> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#gpx_qsubmit/blastdb_dir> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#gpx_qsubmit/ids> ;
        cwl:out  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#gpx_qsubmit/jobs> ;
        cwl:run  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit.cwl> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/ids>
        cwl:linkMerge  "merge_flattened" ;
        cwl:source     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Separate_Plasmid_ORFs/chomosome_orfs> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#cluster_and_qdump/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#asn_cache> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/soft_masking>
        sld:default  "yes" .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#soft_masking>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-soft_masking" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-soft_masking" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#taxon_db>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#max_target_seqs>
        sld:type  xsd:int .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#split_jobs>
        cwl:in   <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#split_jobs/nchunks> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#split_jobs/input> ;
        cwl:out  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#split_jobs/jobs> ;
        cwl:run  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/split_jobs/split.cwl> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#extra_coverage>
        sld:type  xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#max_batch_length>
        sld:type  xsd:int .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Map_Naming_Hits/align_fmt>
        sld:default  "seq-align-set" .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_struct.cwl#blast_type>
        sld:type  xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/bacterial_hit_mapping.cwl#expansion_ratio>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-expansion-ratio" ] ;
        sld:type          xsd:float .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#prot_ids_B2>
        rdfs:label  "AntiFam tainted proteins I/oseqids" ;
        sld:type    cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/nogenbank>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#nogenbank> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#raw_seqs>
        rdfs:label  "Prepare_Unannotated_Sequences/sequences" ;
        sld:type    cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/scatter_gather_nchunks>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#scatter_gather_nchunks> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/word_size>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#word_size> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#taxon_db>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#split_jobs>
        cwl:in   <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#split_jobs/nchunks> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#split_jobs/input> ;
        cwl:out  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#split_jobs/jobs> ;
        cwl:run  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/split_jobs/split.cwl> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/orf_hits_cache_retrieve.cwl#sqlite_cache>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-blast-hits-sqlite-cache" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/evalue>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#evalue> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#cluster_and_qdump/top_by_score>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#top_by_score> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#blast_type>
        sld:type  xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/cluster_blastp_wnode.cwl#input_jobs>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input-jobs" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input-jobs" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#sequence_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#unicoll_cache> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/split_jobs/cat_array_of_files.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "file concatenation" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "cat" ) ;
        cwl:baseCommand          ( "cat" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/split_jobs/cat_array_of_files.cwl#files_in> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/split_jobs/cat_array_of_files.cwl#file_out> ;
        cwl:stdout               "cat.out" .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#batch-size>
        sld:type  xsd:int , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/affinity>
        sld:default  "subject" .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#cluster_blastp_wnode/extra_coverage>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_cluster_and_qdump.cwl#extra_coverage> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Naming_Protein_Hits_for_struct/blastdb>
        cwl:linkMerge  "merge_flattened" ;
        cwl:source     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#blastdb> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#blast_rules_db> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/extra_coverage>
        sld:default  29 .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/bacterial_hit_mapping.cwl#no_compart>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-no-compart" ] ;
        sld:type          xsd:boolean .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass2.cwl#Find_Struct_Protein_Hits_for_Plasmids/soft_masking>
        sld:default  "yes" .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#retrieve_cached_hits/sqlite_cache>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#blast_hits_cache> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#gpx_qsubmit/max_batch_length>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_blastp_wnode_naming.cwl#max_batch_length> .